Research workbench
Crystal structure of the E45N mutant from kdpg aldolase from escherichia COLI
Analyse Crystal structure of the E45N mutant from kdpg aldolase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WBH
- Type
- protein
- Length
- 640 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KHG/KDPG aldolase
- EC
- 4.1.2.14
- UniProt
- P10177
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | KHG/KDPG aldolase (EC 4.1.2.14) | protein | 213 | 45% helix, 17% strand | P10177 |
| B | KHG/KDPG aldolase (EC 4.1.2.14) | protein | 214 | 43% helix, 17% strand | P10177 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.76 | 0.91 | 28 | empty |
| 2 | 110 | 0.69 | 0.91 | 27 | empty |
| 3 | 84 | 0.42 | 0.79 | 29 | PO4 |
| 4 | 95 | 0.40 | 0.77 | 18 | PO4 |
| 5 | 98 | 0.36 | 0.75 | 20 | PO4 |
Interfaces
3 interfaces between chains.
- B–C · 600 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 599 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 588 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1WBH · Crystal structure of the E45N mutant from KDPG aldolase from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P10177
- Elsewhere: RCSB PDB 1WBH · PDBe 1WBH · UniProt P10177
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